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MsaToVcf

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Pierre Lindenbaum edited this page Feb 3, 2016 · 3 revisions

DEPRECATED use https://github.com/sanger-pathogens/snp_sites

##Motivation

Getting a VCF file from a CLUSTAW alignment. See also http://www.biostars.org/p/94573/

input is a clustalw file like: https://github.com/biopython/biopython/blob/master/Tests/Clustalw/opuntia.aln

##Compilation

See also Compilation.

$ make msa2vcf

##Synopsis

the clustalw file at https://github.com/biopython/biopython/blob/master/Tests/Clustalw/opuntia.aln

$ java -jar dist/msa2vcf.jar (stdin|file.aln)

##Options

Option Description
-R (name) Reference name (optional) used in the VCF/contig
-f (name) Save fasta sequences in this file (optional)
-m Haploid output
-a print ALL positions
-c (name) sepcify 'name' as consensus/reference sequence.
-h get help (this screen) and exit.
-v print version and exit.
-L (level) log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/msa2vcf/MsaToVcf.java

##Example

$ curl https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln

CLUSTAL W (1.81) multiple sequence alignment


gi|6273285|gb|AF191659.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273284|gb|AF191658.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273287|gb|AF191661.1|AF191      TATACATTAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273286|gb|AF191660.1|AF191      TATACATAAAAGAAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273290|gb|AF191664.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273289|gb|AF191663.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
gi|6273291|gb|AF191665.1|AF191      TATACATTAAAGGAGGGGGATGCGGATAAATGGAAAGGCGAAAGAAAGAA
                                    ******* **** *************************************

gi|6273285|gb|AF191659.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273284|gb|AF191658.1|AF191      TATATATA--------ATATATTTCAAATTTCCTTATATACCCAAATATA
gi|6273287|gb|AF191661.1|AF191      TATATA----------ATATATTTCAAATTTCCTTATATATCCAAATATA
gi|6273286|gb|AF191660.1|AF191      TATATA----------ATATATTTATAATTTCCTTATATATCCAAATATA
gi|6273290|gb|AF191664.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273289|gb|AF191663.1|AF191      TATATATATA------ATATATTTCAAATTCCCTTATATATCCAAATATA
gi|6273291|gb|AF191665.1|AF191      TATATATATATATATAATATATTTCAAATTCCCTTATATATCCAAATATA
                                    ******          ********  **** ********* *********

gi|6273285|gb|AF191659.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCCATTGATTTAGTGT
gi|6273284|gb|AF191658.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273287|gb|AF191661.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273286|gb|AF191660.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273290|gb|AF191664.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
gi|6273289|gb|AF191663.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTAT
gi|6273291|gb|AF191665.1|AF191      AAAATATCTAATAAATTAGATGAATATCAAAGAATCTATTGATTTAGTGT
                                    ************************************ *********** *

gi|6273285|gb|AF191659.1|AF191      ACCAGA
gi|6273284|gb|AF191658.1|AF191      ACCAGA
gi|6273287|gb|AF191661.1|AF191      ACCAGA
gi|6273286|gb|AF191660.1|AF191      ACCAGA
gi|6273290|gb|AF191664.1|AF191      ACCAGA
gi|6273289|gb|AF191663.1|AF191      ACCAGA
gi|6273291|gb|AF191665.1|AF191      ACCAGA
                                    ******

generate the VCF

$ curl https://raw.github.com/biopython/biopython/master/Tests/Clustalw/opuntia.aln" |\
  java -jar dist/msa2vcf.jar

##fileformat=VCFv4.1
##Biostar94573CmdLine=
##Biostar94573Version=ca765415946f3ed0827af0773128178bc6aa2f62
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth.">
##contig=<ID=chrUn,length=156>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	gi|6273284|gb|AF191658.1|AF191	gi|6273285|gb|AF191659.1|AF191	gi|6273286|gb|AF191660.1|AF191	gi|6273287|gb|AF191661.1|AF191	gi|6273289|gb|AF191663.1|AF191	gi|6273290|gb|AF191664.1|AF191	gi|6273291|gb|AF191665.1|AF191
chrUn	8	.	T	A	.	.	DP=7	GT:DP	0:1	0:1	1:1	0:1	0:1	0:1	0:1
chrUn	13	.	A	G	.	.	DP=7	GT:DP	0:1	0:1	0:1	0:1	1:1	1:1	1:1
chrUn	56	.	ATATATATATA	ATA,A,ATATA	.	.	DP=7	GT:DP	1:1	2:1	2:1	2:1	3:1	3:1	0:1
chrUn	74	.	TCA	TAT	.	.	DP=7	GT:DP	0:1	0:1	1:1	0:1	0:1	0:1	0:1
chrUn	81	.	T	C	.	.	DP=7	GT:DP	0:1	0:1	0:1	0:1	1:1	1:1	1:1
chrUn	91	.	T	C	.	.	DP=7	GT:DP	1:1	1:1	0:1	0:1	0:1	0:1	0:1
chrUn	137	.	T	C	.	.	DP=7	GT:DP	0:1	1:1	0:1	0:1	0:1	0:1	0:1
chrUn	149	.	G	A	.	.	DP=7	GT:DP	0:1	0:1	0:1	0:1	1:1	0:1	0:1

##See also

##History

  • Dec 2015: renamed msa2vcf
  • Aug 2015: added option -a https://github.com/lindenb/jvarkit/issues/30 and added option -c 'consensus-name'
  • July 2015: fixed clustal bug: consensus was wrong when there was no consensus, sometimes, in some blocks. (via Vanessa Goncalves)
  • Feb 2015: support for lines starting with "CLUSTAL 2"
  • Nov 2014. alleles in VCF should be homozygotes thanks to diviya.smith@biostars : https://www.biostars.org/p/94573/#118617
  • 2014: Creation

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License

The project is licensed under the MIT license.

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